Graph

Graph: Select type of graph.

• GC content: Percentage of guanines and cytosines in each window, given by (G + C) / (G + C + A + T) where G, C, A and T are the count of each nucleotide.

• GC skew: Ratio of guanines to cytosines in each window, given by (G – C) / (G + C).

• Coverage: If provided with an ACE file in the input file field, Easyfig will calculate the coverage across each contig, and plot it against the first identical sequence found in the feature file. Can only be used with the top genome.

• Custom: Plots a custom graph. Input is a plain text file with a single column of numbers, one line per data point.

If more datapoints are provided than the width of the image, datapoints correlating to each pixel will be averaged.

Multiple graphs: If unchecked only the top sequence file will be graphed. If checked all sequence files will be graphed. To plot multiple custom graphs, the input file should have numbers in columns separated by tabs for each sequence file to be plotted.

Input file: Give the filename of the user created custom file, or an ACE file.

Step: Generate a data point every x base pairs.

Window size: Amount of bases adjacent to each step to calculate GC content/skew. This is the amount of bases in total to be counted i.e. 1000 counts 500 bases to each side of the step position.

Maximum Y: maximum value of the Y axis. If set to “Auto� this will be set to the maximum of the Y axis will be set as the maximum Y value.

Log Scale (log 10): Make the Y axis log10 scaled. Useful for high coverage data.

Graph type: Choose histogram or line graph.

Axis line thickness: Thickness of the x axis line in pixels.

Positive value colour: Colour of the line or histogram bars with positive y values or GC content greater than 50%.

Negative value colour: Colour of the line or histogram bars with negative y values or GC content lower than 50%.

Gap between graph and figure: Gap in pixels between the graph and the annotation and comparison drawings.